 |
 |
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Feb 24, 2017 |
Title |
ASXL1_WT_ChIPseq |
Sample type |
SRA |
|
|
Source name |
hematopoietic stem/progenitor cells
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: Bone Marrow cell type: BM-derived Lin-Kit+ cells
|
Extracted molecule |
genomic DNA |
Extraction protocol |
LK cells were fixed with 1% formaldehyde, lysates were sonicated and the DNA was sheared to an average length of 300 to 500 bp. Protein-DNA complexes were isolated with specific antibodies. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
ASXL1_i94
|
Data processing |
Basecalls performed using Illumina NextSeq 500 ChIP-Seq reads were aligned to the mm10 genome assembly using the BWA algorithm with default settings Data were filtered using the following specifications:only reads that pass Illumina's purity filter,aligned with no more than 2 mismatches,and map uniquely to the genome were used in the subsequent analysis,than duplicate reads were removed. peaks were called using SICER version 1.1 with the following setting:Threshold for redundancy allowed for ChIP reads(1),window size(200bp) ,FDR cutoff(1E-10) Genome_build: mm10 Supplementary_files_format_and_content: bigWig file
|
|
|
Submission date |
Jul 01, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Peng Zhang |
E-mail(s) |
pxz36@miami.edu
|
Organization name |
University of Miami Miller School of Medicine
|
Lab |
Feng-Chun Yang
|
Street address |
1011 NW 15th Street
|
City |
Miami |
State/province |
FL |
ZIP/Postal code |
33136 |
Country |
USA |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE83960 |
ASXL1 Interacts with the Cohesin Complex to Maintain Chromatid Separation and Gene Expression for Normal Hematopoiesis [ChIP-Seq] |
GSE83962 |
ASXL1 Interacts with the Cohesin Complex to Maintain Chromatid Separation and Gene Expression for Normal Hematopoiesis |
|
Relations |
BioSample |
SAMN05341301 |
SRA |
SRX1892693 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2224545_10_2470IUPUI_WT_BM_ASXL1_i94_uniqnorm_signal.bw |
158.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
 |